Add null check
Purge coverage periodically
Increase number of spans to keep in memory
Optimizing rum2cov some
Add some logging
Merge branch 'master' of github.com:PGFI/rum
Fix compile error in RUM::Mdust
Bump version number to v2.0.3_05
Fix manifest
Fix #143: allow user to specify qsub options

You can now pass in additional options to qsub using
--platform-options. Please see "rum_runner help align" for
more information.

Also, we now use "-pe make 2" as the default for qsub, which
reserves 2 slots.
Bump version number to 2.0.3_06
Change sam2xs-tag to not skip over header lines
Add script to show config info
Restore input file check

It was commented out for some reason
Bump version number to 2.0.4.
Change show_config to not validate the config
Make sort_rum_by_id use strict
Change sort_RUM_by_id to check output file size

Output file should be the same size as input file. This is an
easy check to do to make sure none of the temporary files got
corrupted.
Make rum2sam explicity check for corrupt input

We've seen a few cases where sort_RUM_by_id.pl produces files
that have more or less fields than they should on a few lines.
This can cause rum2sam to enter an infinite loop. I'm adding a
check every time we read a line in to make sure that it at least
has the right number of fields.
Always re-download organisms.txt file